Canadian &

A Sector Strategy led by Genome Atlantic and Genome British Columbia, with support from regional Genome Centres across Canada How genomics can address and funded by Genome Canada. sector challenges August 2013 Genomics* is the science that aims to decipher Genome Canada and the six regional Genome Centres and understand the entire genetic information of across the country are working to harness the transfor- an organism (i.e. microorganisms, plants, animals mative power of genomics to deliver social and and humans) encoded in DNA and corresponding economic benefits to Canadians. complements such as RNA, proteins and metabolites. This paper is one in a series of four sector strategies The knowledge and innovations emerging from funded by Genome Canada and co-led by the Genome this field are finding solutions to complex biological Centres. They include: Agri-Food, Energy and Mining, challenges, while at the same time raising questions Fisheries and Aquaculture, and Forestry. Each strategy, of societal and economic importance. developed in consultation with sector stakeholders, maps out how the sector can further leverage the Genomics has already brought huge economic and transformative power of genomics, and related disci- societal gains to Canadians through better healthcare, plines, to its advantage. improving food quality, safety and production and protecting our environment and natural resources. Given Canada’s footprint in these key natural resource sectors, the time is ripe for our industries to take full Looking ahead, genomics will be the foundation of advantage of the power and promise of genomics. Canada's growing bio-economy (all economic activity derived from life science-based research), which is *Broadly speaking, our definition of genomics includes estimated to be responsible for some 2.25 per cent related disciplines such as bioinformatics, epigenomics, of GDP, or about $38 billion, by 2017. metabolomics, metagenomics, nutrigenomics, pharma- cogenomics, proteomics and transcriptomics. Increasingly, genomics is equipping a range of Canadian industries—agriculture, energy, mining, forestry, fisheries For more information, visit and aquaculture and health, among others—with cutting- www.genomecanada.ca/en/sectorstrategies edge science and technologies. This is driving growth, productivity, commercialization and global competitive- ness, while finding solutions to environmental sustainability problems.

Prepared by David H. Millar, Haisley Millar Consulting Group, Inc. Published by Genome Canada, 2013 ©Genome Atlantic and Genome British Columbia 2013

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Table of Contents 1. Executive Summary...... 2 2. The Importance of the Fisheries and Aquaculture Sector to the Canadian Economy...... 4 2.1 Commercial Fisheries...... 4 2.2 Recreational Fisheries...... 6 3. Challenges in the Fisheries and Aquaculture Sector...... 7 3.1 Common Challenges...... 7 3.2 Challenges for Commercial Fisheries...... 8 3.3 Challenges in Aquaculture...... 9 3.4 Challenges For Recreational Fisheries...... 10 4.The Role of Genomics in Mitigating the Challenges and Creating the Opportunities...... 11 4.1 Expanding Genomics Knowledge and its Use...... 11 4.2 Food Production...... 11 4.3 Fish Health...... 12 4.4 Conservation and Population Genomics...... 12 4.5 Ecosystem Integrity...... 13 4.6 Social Licence...... 14 5. Canada’s Leadership and Strengths...... 15 5.1 Canada’s Investment...... 15 5.2 Canada’s Leadership...... 16 6. Success of Past Canadian Investments in Fisheries & Aquaculture Genomics...... 17 7. The Socio-Economic Impact of Successful Genomics Enabled Solutions...... 20 7.1 Commercial Fisheries...... 20 7.2 Recreational Fisheries...... 21 8. Next Steps Toward Success...... 22 Acknowledgements...... 24 1. Executive Summary

In 2012–2013 key stakeholders across Canada were Fisheries and aquaculture is a global sector of strategic consulted as to the challenges and genomics opportuni- importance to Canada. Capture fisheries and aquaculture ties for the fisheries and aquaculture sector. Individuals supplied the world with about 148 million tonnes (Mt) of representing industry, government, and academia were fish and fish protein in 2010 valued at $217.5 billion. contacted, and invited to participate in a national Of this, global capture fisheries contributed about workshop, entitled Canadian Fisheries and Aqua- 90Mt and farmed fish production around 60Mt. Capture culture: A Strategy to Increase Competitiveness fisheries has, in all likelihood, reached its maximum and Sustainability through the Application of global limit, and over 70 percent of the world’s marine Genomics, held on April 11–12, 2013 in Toronto. stocks or species groups are either fully-exploited, The event was hosted by Genome Atlantic and Genome over-exploited or are depleted/recovering stocks.3, 4 It BC with support from Genome Canada and other is generally agreed that the global marine system is Genome Centres. Prior to the workshop, participants overstressed, experiencing a reduction in biodiversity were provided with a copy of a Draft Genomics Sector and is anthropogenically challenged. Its major chal- Strategy Paper, which was based on the extensive lenge and focus are conservation and sustainable consultation and research process that took place marine biodiversity. Global farmed fish production is during 2012–2013. growing at 6.3 percent per year and priorities are increasingly being directed to achieving efficient, “Genomics—a vital link in the future success safe (most farmed fish is for human consumption), of Canadian fisheries and aquaculture” high-quality, and economic food protein production The application of genomics1 has the potential to provide that has minimal impact on the ecosystems with Canada’s commercial2 and non-commercial fisheries with which it interfaces. the tools to support strong, competitive growth based on Canada has 25 percent (243,000 km) of the world’s product quality and security, technological soundness, coastline, on the Atlantic, Northern and Pacific coasts, economic viability, environmental integrity and social an exclusive economic zone encompassing some licence. The cross-cutting theme of this Fisheries and 3.1 million km2, and 16 percent of the world’s fresh Aquaculture Genomics Sector Strategy 2013 water. In total, commercial and non-commercial Paper is that the genome sciences can, and should, fisheries contribute $14.7 billion annually to the support and inform the sustainable development and Canadian economy and support over 130,000 jobs. management of Canada’s aquatic ecosystems and Yet Canada produces less than one percent of the resources to the benefit of its people, its natural world’s fisheries (capture and farmed) product. resources and the national economy.

1 Genomics is defined as a branch of biotechnology concerned with applying the techniques of genetics and molecular biology to the genetic mapping and DNA sequencing of sets of genes or the complete genomes of selected organisms, with organizing the results in databases, and with applications of the data. The genome sciences include disciplines such as, genomics, transcriptomics, proteomics, metabolomics, metagenomics, systems biology and bioinformatics. 2 Commercial is defined as aquaculture production and capture (wild) fisheries landings; non-commercial is defined as recreational, cultural and subsistence fishing. 3 The State of World Fisheries and Aquaculture, 2012, FAO 4 Review of the Status, Trends and Issues in Global Fisheries and Aquaculture, with Recommendations for USAID Investments, USAID SPARE Fisheries & Aquaculture Panel

2 Genome Atlantic and Genome British Columbia A modest increase in market share would result Canada’s track record of research success and excellence in substantial economic and social gains for in fish genomics has been well supported with investments Canada’s industry, and its coastal, rural and by industry and government. Genomics can play a major Aboriginal communities. part in breeding the best species for commercial and non-commercial use, and can ensure that this is done Supported by funding from Genome Canada, large-scale in a sustainable manner, protecting and conserving projects such as the Atlantic Cod Genomics and Brood- the aquatic ecosystem of Canada’s oceans, lakes and stock Project (CGP), Pleurogene (Halibut genomics), the rivers. From the national workshop, five key research Genomic Research on Atlantic Salmon Project (GRASP) themes emerged to achieve economic, social and and its successor, the Consortium for Genomic Research environmental sustainability: on all Salmonids Project (cGRASP), have resulted in Canada’s recognition as a global leader in fish genomics. 1 Translational research: a continued focus on Researchers are supported by a first-class research outcome-based genomics research, especially with infrastructure encompassing universities, research respect to , new and invasive species; institutes, and federal research labs, as well as innova- tive companies. Success in the sustainable development 2 Genomics tools: the development of practical, and management of aquatic ecosystems will depend affordable, and trusted genomic diagnostics; on reducing uncertainty and having a better knowl- 3 Health and nutrition: ensuring the conservation edge of the impacts of highly complex issues such as of wild stocks and satisfying the needs of consum- climate change, anthropogenic forces, disease, popula- ers for quality protein, and to understand disease tion genetics, biodiversity, and wild and farmed fish mechanisms and the determinants of stress; interfaces. The application of Canada’s fisheries and aquaculture genomics capacity to these challenges will 4 Species sustainability: safeguarding the survival support industry, communities and government to make and conservation of aquatic species–both fin and strategic decisions based on sound scientific knowledge. shellfish–is vital to the maintenance of a thriving aquatic ecosystem and the Canadian fisheries and Clearly, and as shown above, there has been successful aquaculture sector; and funding into genomics in Canada. However, would further investment in a genomics strategy for fisheries 5 Breeding programs: from high-quality seedstock and aquaculture be good for Canada? Investors look for hatcheries to elite for farms, breeding for a select range of key indicators: global market size programs are essential for effective management, and growth potential, stable regulatory situation with species planning and control of the outputs. timely decision approvals, investor certainty, security of Genomics in the fisheries and aquaculture sector can, tenures, a team with a record of success, commitment and should, support the balance between the need for from the principals, the ability to differentiate the economic and production efficiency, with social licence product from competitors, and in the case of the and the consent of the community, and the sustainabil- capture a sustainable supply. As evidenced ity of the aquatic ecosystem. It is indeed “a vital link in by production and consumption data and ongoing the future success of Canadian fisheries and aquacul- investments by other nations, the global fisheries and ture” and a worthwhile investment for Canada. aquaculture sector will continue to exhibit excellent growth characteristics and provide an excellent return on investment.

Canadian Fisheries & Aquaculture How genomics can address sector challenges 3 2. THE IMPORTANCE OF THE FISHERIES AND AQUACULTURE SECTOR TO THE CANADIAN ECONOMY The majority of the substantial impacts and benefits 2.1.1 Commercial Capture Fisheries that fisheries and aquaculture generates for Canada are experienced in and by rural, coastal and First In 2011, commercial sea and freshwater fisheries’ Nations communities—in every province and territory. landings (including shellfish) totalled $2.2 billion and the industry employed over 50,000 fish harvesters 2.1 Commercial Fisheries and crew. Between 1990 and 2011, Canadian catches from capture9 fisheries increased in value by 41 percent, Commercial (sea and freshwater) fisheries, aquaculture but declined 48 percent by weight. The decline in finfish and processing contribute $6.4 billion in outputs landings was mitigated by an increase of 72 percent (landings, production and processing), over 80,000 jobs by volume, and 220 percent by value, for shellfish and a positive trade balance of $1.5 billion to the landings. Shellfish now account for around 50 percent 5 Canadian economy. of the total volume and 77 percent of the value of Integration of First Nations Fisheries is a national landings. Lobster, shrimp and queen crab alone priority. The Atlantic and Pacific Integrated Commercial account for almost 70 percent of the value of total 10 Fisheries Initiatives6, 7 are designed to integrate First commercial landings. Nations fishing enterprises into existing commercial In 2011, according to Fisheries and Oceans Canada fisheries in order to provide economic opportunities (DFO), 84.5 percent of value and 82.4 percent of for First Nations fishermen and to improve the overall volume of seafisheries (finfish and shellfish) landings management of fisheries on the Atlantic and Pacific originated from Eastern Canada11 with the remainder coasts. To date the Government has invested over from BC. In shellfish landings, 93 percent of value and $730 million to provide First Nations access to com- 98 percent of volume are from Eastern Canada. East mercial fisheries and to assist in building sustainable coast fisheries have much wider species diversity in commercial fisheries enterprises. Canada’sEconomic comparison to the West coast: around 13 species are 8 Action Plan 2013 proposes to provide $33.1 million the foundation of the East coast fisheries and include in 2013–14 to Fisheries and Oceans Canada to extend groundfish species such as cod, haddock, halibut, the Atlantic and Pacific Integrated Commercial Fisher- redfish (rockfish), flatfishes, Greenland turbot, pollock ies Initiatives. and hake, and pelagic species such as herring, mackerel, swordfish, tuna and capelin. The highest value finfish in

5 http://www.dfo-mpo.gc.ca/stats/facts-Info-11-eng.htm 6 http://www.dfo-mpo.gc.ca/fm-gp/aboriginal-autochtones/aicfi-ipcia/index-eng.htm 7 http://www.pac.dfo-mpo.gc.ca/index-eng.html 8 http://actionplan.gc.ca/en 9 For the purposes of this paper, “capture” and “wild” are equivalent terms 10 DFO, Ottawa 11 New Brunswick, Newfoundland and Labrador, Nova Scotia, Prince Edward Island and Quebec

4 Genome Atlantic and Genome British Columbia Eastern Canada is Greenland turbot, followed by herring than 160,000t per year from 2007 to 2011. Industry and halibut; the species with the highest volume of believes that opportunities for expansion and strong landings is herring which at 141,929t is almost three production growth remain, although this assumes a times that of hake, its closest rival.12 West coast fisher- favourable business environment and an appropriate ies are concentrated on redfish (rockfish), flatfishes, federal legislative framework to restore investor halibut, hake, herring, tuna, and salmon. Hake is the confidence.16,17 highest volume of landings followed by salmon and redfish, while, by value, salmon remains the leader Salmon remains the main species produced, contributing followed by halibut and tuna. Landings of salmon have 63 percent of total (finfish and shellfish) production declined five-fold, by volume, since 1990, with 2011 volume, followed by shellfish ( and ) figures showing landings at 20,417t with a value of at 22 percent. It makes up 83 percent of finfish $46 million.13, 14, 15 aquaculture production, and is predominantly located in BC, which accounts for 73 percent of production, 2.1.2 Aquaculture followed by New Brunswick (NB), Newfoundland and Labrador (NL) and Nova Scotia (NS). Trout is second, The aquaculture industry provides 15,000 jobs (direct, providing 5.3 percent of production in 2011. It has indirect and induced) with operations in every province, shown 6 percent growth per year since 2007 and is as well as the Yukon. It has a gross value of more than mostly located in Ontario.18 $2.1 billion and provides around $1 billion toward Canada's gross domestic product. Globally, Canada’s aquaculture production represents less than one percent of world aquaculture production. Between 2001 and 2011, Canadian aquaculture It produces 6.25 percent of the Americas’ output, production increased 40 percent by value to $846M, ranking 5th behind Chile, the United States (U.S.), while production volume increased by just 6 percent. Brazil and Ecuador. With respect to high-value species, Harvested production has not demonstrated significant Canada’s performance trends slightly more positively. growth in the past decade, due in part in British Colum- For example, it accounts for 8 percent of global bia (BC) to regulatory controls, and has averaged less

12 Ibid 13 The decline in the sockeye population in 2008 prompted the setting up in 2009 of the Cohen Commission of Inquiry into the Decline of Sockeye Salmon in the Fraser River. The Commission’s report was released in October 2012 14 http://www.dfo-mpo.gc.ca/stats/commercial/sea-maritimes-eng.htm 15 DFO, Ottawa 16 Aquaculture in Canada 2012, A Report on Aquaculture Sustainability, DFO 17 Aquaculture Statistics, 2011, Statistics Canada, November 2012 18 Aquaculture Statistics, 2011, Statistics Canada, November 2012

Canadian Fisheries & Aquaculture How genomics can address sector challenges 5 farmed-salmon production ranking 4th behind Norway, popularity needs quantitative study, but various authors the United Kingdom and Chile. Given Canada’s consid- suggest issues such as changing angler demographics, erable natural assets, world-class companies, and damage or deterioration of the habitat, over-fishing, research excellence, there is little doubt that its declining fish populations and an absence of management aquaculture industry has the potential to surpass its resources to fully assess status, as contributing factors. current production.19, 20, 21, 22 Over 80 percent of freshwater fish landed in 2011 2.2 Recreational Fisheries were from five species. In order, these were walleye (yellow pickerel), whitefish, perch, pike and white In 2010, Canada’s recreational fishing contributed bass.26 These and other species such as wild salmon, 23 $8.3 billion to the national economy and supported trout (Brook Trout in particular) and Arctic charr are 24 over 50,000 jobs. It attracts a high level of inward critical to the sustainability of recreational fishing, investment, with almost $140 million invested by which is, in turn, a key component of nature-based non-residents and foreign anglers in 2010. tourism in many provinces and the Northern Territories. The segment is highly diffuse, located in small clusters For example, in 2001, in BC, salmon sport fishing with few major players. Overall, the popularity of angling accounted for approximately $231 million in output, is declining by an estimated 2 percent per year contributed $116 million to provincial GDP, and 27 28,29 (domestic anglers) and 35 percent (visiting anglers) provided 2,280 full-time equivalent jobs. although this has been compensated for by increased per capita spending.25 The reason for the decrease in

19 Socio-Economic Impact of Aquaculture in Canada; prepared for Fisheries and Oceans Canada by GardnerPinfold Consulting Economists Ltd., 2010 20 Report to Launch the Aquaculture Sustainability Reporting Initiative, DFO, 2010 21 The State of World Fisheries and Aquaculture, 2012, FAO 22 http://www.canadainternational.gc.ca/norway-norvege/commerce_canada/aquanor07/aquaculture.aspx?view=d 23 This is made up of $5.8 billion in investment and $2.5 billion in direct spending. (It should be noted that the contribution of the commercial fisheries industry is primarily based on landings value and tonnage and hence direct comparison between the recreational and commercial sectors is not possible based on current reporting data.) 24 Likely due to its diffuse nature, there is a lack of up to date information on recreational fishing jobs. However, the Canadian Sport Fishing Association in 2000 put the figure at 47,400 jobs. A 2010 paper A global estimate of benefits from ecosystem-based marine recreation: potential impacts and implications for management, Andrés M. Cisneros-Montemayor and U. Rashid Sumaila, J Bioecon, published online August 2010 cited that in the U.S., $43,000 in direct expenditure on recreational fishing generates one full time job. Applying this to Canada’s direct spending on recreational fishing of $2.5 billion would suggest about 55,000 jobs created. 25 Survey of Recreational Fishing in Canada 2010, DFO 26 DFO Statistics Branch 27 A full-time equivalent (FTE) job is a better measure of labour inputs to production, i.e., productivity. In Canada, one full-time equivalent is 40 hours per week. 28 Economic Value of the Commercial Nature-Based Tourism Industry in British Columbia. Pacific Analytics and Tourism British Columbia, in cooperation with the Wilderness Tourism Association, 2004 29 Special Committee on Sustainable Aquaculture, Legislative Assembly of the Province of British Columbia, May 2007. Final Report, P.1.

6 Genome Atlantic and Genome British Columbia 3. CHALLENGES IN THE FISHERIES AND AQUACULTURE SECTOR The key challenge for Canada is how its fisheries and 3. Ecosystem sustainability: maintaining healthy aquaculture sector can grow economically and effi- and productive ecosystems and animals, monitoring ciently, while managing its aquatic resources in a climate change impacts on the aquatic ecosystem, sustainable manner. A secondary challenge is the the role of aquatic species in environmental generation and application of information and tools toxicology, species welfare and biodiversity and to monitor and measure impacts, mitigate uncertainty, fisheries management; and provide decision-makers (government, industry and community) with a sound scientific basis for 4. Supporting food safety: product traceability, fish policies, regulations and programs. forensics, ensuring safe and healthy products, and understanding zoonotic disease transmission;

3.1 Common Challenges 5. Production sustainability and resource While they may have differing needs and priorities, it is efficiency:monitoring biophysical capacity; also true to state that capture, farmed and recreational stockholding and alternate rearing environments; fisheries have significant economic, biological and maintaining animal health and welfare through the ecosystem interfaces and the sustainability of one development, validation and commercialization of may have an impact on either or both of the remaining vaccines and understanding host-pathogen rela- segments. The arrays of challenges that face the tionships; and continuing the reduction of inputs overall sector and on which genomics can make a such as feed; significant impact include: 6. Social licence: genomics and its related ethical, 1. Understanding of genomics: a key theme arising environmental, economic, legal and social aspects from the strategy workshop was that nationally the (GE3LS) approaches need to be applied to a wide level of understanding of genomics and genomics range of issues such as: encouraging stakeholder tools within the sector is generally poor. Growers social responsibility and awareness; supporting and fishers do not understand the science, the tools certification, regulation, policy and national sustain- or their application; industry and academia are not ability initiatives; ensuring an economically viable fully informed as to the availability of genomics and competitive industry; communicating risk, assets; and the public lacks access to good, inde- i.e., ensuring that the public and other user groups pendent information and so makes judgments understand what can be expected from genomics- based on the outputs of well-funded, special based activities and that policy makers are informed interest groups. There is also a lack of understand- of these views; supporting targeted, impactful ing of the economics of the application of genomic research through better industry-academia collabo- tools, i.e., the cost of development versus the rations and ensuring that translation of genomics benefits derived; research excellence benefits Canada; and inform- ing the public and industry of the benefits of 2. Meeting market demand: raises issues such as, genomics-based tools and approaches. increased production efficiency and product quality; sustainable harvesting; species exploitation; and the globalization of food production and distribution;

Canadian Fisheries & Aquaculture How genomics can address sector challenges 7 3.2 Challenges for Commercial Fisheries 4. Conservation genetics: the conservation of wild fish genetic resources (FiGR) is a sustainability 3.2.1 Capture fisheries priority. Genetically diverse populations are more “The goals of conservation and a sustainable likely to survive and adapt to environmental stress wild fishery are complementary. Conserva- and are needed by aquaculture for future breeding tion measures are intended to promote programs, e.g., Atlantic salmon and Arctic charr, abundant, healthy stocks that may in turn where there may be a limited genetic base from permit harvest, while fisheries management which to draw; activities regulate the catch so that future 5. Economic sustainability: achieving economic productivity is assured.”30 sustainability through the production of strong and Specific challenges facing capture fisheries include: sustainable stocks is a key challenge that could be addressed by genomics. However, a further chal- 1. Fish migration: understanding one of the most lenge for capture fisheries is justifying investments complex and intriguing biological phenomena in the in genomics when subsequently, due to ministerial animal kingdom is essential for the conservation of discretion, there may be a lack of access to the species, and its monitoring and management; resource; and

2. Biodiversity: the rate of loss (species and stocks) 6. Fisheries and aquaculture interactions: is estimated to be 100–1000 times greater than competition, feral stock replacement, pathogen natural rates of extinction and it is estimated that transmission between fisheries and aquaculture 31 65 percent are fully- or over-exploited. Biodiversity and vice versa, and genetic interactions all is essential for species survival, and biocomplexity potentially impact the evolutionary trajectory is important for the stability of ecosystem services; of wild fish.32, 33, 34 3. Population genetics: local populations should be conserved, as they provide genetic diversity and are often adapted better to local conditions. There is a genetic basis for local adaptation, but until recently these unique traits, including their plasticity, have been difficult to measure;

30 Cohen Commission of Inquiry into the Decline of Sockeye Salmon in the Fraser River, October 2012 31 Review of the Status, Trends and Issues in Global Fisheries and Aquaculture, with Recommendations for USAID Investments, USAID SPARE Fisheries & Aquaculture Panel 32 The functional genomics of rapid evolutionary changes between domesticated and wild salmon populations, L. Bernatchez and Christian Roberge 33 McGinnity.P et al, Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon, Proc. R. Soc. Lond. B (2003) 270 34 John J. Piccolo and Ewa H. Orlikowska, A biological risk assessment for an Atlantic salmon (Salmo salar) invasion in Alaskan waters, Aquatic Invasions (2012) Volume 7, Issue 2: 259–270

8 Genome Atlantic and Genome British Columbia 3.3 Challenges in Aquaculture reducing the environmental footprint of production; developing more nutritious, sustainable diets and Canada has recognized sustainability as the principal feeds; and developing and validating better treat- goal of aquaculture governance. To this end, imple- ments for disease; mentation of Fisheries and Oceans Canada (DFO)’s Aquaculture Sustainability Reporting Initiative (ASRI) 2. The growth of the shellfish industry: from is seen as a Department priority and consistent with humble beginnings, shellfish are now an important the DFO’s lead role in managing Canada’s aquatic part of the Canadian aquaculture sector. Production resources and ensuring “economically prosperous volume has risen rapidly, particularly on the East maritime sectors and fisheries, safe and secure Coast, but there is a lack of understanding of bivalve waterways, and sustainable aquatic ecosystems for genomics. For example, little is known about disease 35, 36 the benefit of present and future generations”. at the molecular level; the impact of invasive species, climate change and ocean acidification; or the A 2011 review of published literature found that, production of reliable seedstock; while salmon production may be at the higher end 37 of environmental impact , overall aquaculture is more 3. Site productivity: is a limiting factor of growth, efficient and less damaging to the environment com- mostly but not exclusively for shellfish, and overlaps pared to other animal protein production systems such with achieving sustainable development and 38 as beef and pork. The industry’s key challenges are: socio-economic benefit;

1. Improving environmental and economic 4. Biophysical capacity assessment: is a challenge sustainability: a key challenge is the identifica- when determining suitable locations for industry tion of commercially desirable performance traits, growth and expansion; and resolving consumer which will deliver increased production efficiency education and awareness issues; and and profitability, and lead to new market opportuni- ties while supporting the socio-economic well-being 5. Informing policy and regulation: future expansion of coastal communities. of the national aquaculture industry may be limited by the lack of clearly defined, and agreed-upon oversight Other challenges include the interaction between and regulatory environment. environment and health; minimising the potential impact of aquaculture on and the environment while maintaining fish health and quality; reducing inputs and operating costs;

35 Sustaining Canadian Marine Biodiversity, an Expert Panel Report on Sustaining Canada's Marine Biodiversity: Responding to the Challenges Posed by Climate Change, Fisheries, and Aquaculture, Prepared by the Royal Society of Canada: The Academies of Arts, Humanities and Sciences of Canada, February 2012 36 Report to Launch the Aquaculture Sustainability Reporting Initiative, DFO, 2010 37 Salmon production methods in northern Europe, Canada and Chile are also considered to more efficient than those in China and other Asian countries (in terms of acidification, climate change, energy demand and land occupation). 38 Hall, S.J., et al, 2011. Blue Frontiers: Managing the Environmental Costs of Aquaculture. The WorldFish Center, Penang, Malaysia.

Canadian Fisheries & Aquaculture How genomics can address sector challenges 9 3.4 Challenges for Recreational fisheries 3. Stocking programs: some of the most important recreational fisheries are supported by massive In recreational fisheries, opportunities for genomics to stocking programs where domestic (captive-reared) play a significant role include addressing challenges fish may interact with their wild counterparts. Yet such as: little is known regarding these interactions, the 1. Ecosystem impacts: there is little understanding costs vs. benefits of stocking practices or the of the impacts of climate change, anthropogenic effectiveness of hatcheries; contamination, and ecosystem interactions; 4. Cultural and subsistence fisheries: 2. Species selection: the breeding and/or introduction non-commercial species are important from an of high efficiency/low environmental impact fish ecosystem perspective, yet little work has been strains, and monitoring ‘catch and release’ stresses on undertaken to understand their importance in terms the aquatic ecosystem are two challenges that could of ecological, cultural and subsistence functions be addressed by a genomics approach; and how genomics can support these species.

10 Genome Atlantic and Genome British Columbia 4. THE ROLE OF GENOMICS IN MITIGATING THE CHALLENGES AND CREATING THE OPPORTUNITIES Expansion of the global library of scientific knowledge 4.2 Food production is a valid output of research, however an applied focus Food production is a real opportunity for Canada’s is needed to integrate Canada’s academic research research capacity to work with industry in an area that excellence in fisheries and aquaculture genomics with can produce long-term impacts and benefits. The corporate innovation and technology deployment, and to application of the genome sciences and genomics achieve aquatic ecosystem and resource sustainability. tools to the identification of valuable performance traits, and their incorporation into selective breeding 4.1 Expanding fish genomics knowledge programs (SBPs); managing disease; optimizing diets and its use and feed; and ensuring hatchery effectiveness are The Precautionary Approach adopted by the Government clear opportunities. of Canada seeks to classify the status of a fish stock based on a scientific analysis of biological indicators. The economic argument for SBPs using marker assisted This is a driver in support of better and timely genom- selection (MAS) is very strong, with investments in ics information to help achieve Canada’s conservation efficient breeding programs having benefit to cost ratios and management goals. For industry, the application ranging from 8:1 to 60:1.39 Yet 90% of global aquacul- of genomic research is no less important although its ture is still based on wild and genetically unimproved main driver is economic sustainability. animals. Norway has a national aquaculture breeding program that now includes economically important The timely access to research databases, dissemination traits such as age at sexual maturation, resistance to of tools, expertise and assets is a key criterion for good disease, fillet colour, fillet fat content and distribution, science. High quality reference genome sequences, and and body shape. SBPs in Canada are led by compa- high density marker development, validation and applica- nies such as Cooke Aquaculture40, Marine Harvest tion continue to be critical to the translation of genomic Canada41, Icy Waters42, Grieg and Mainstream discovery to improved animal production and health. Canada43 who has the longest running, most advanced Genetic stock identification technologies and data- Atlantic salmon breeding programs in Canada. Other key bases need to be developed and populated, and basic genomics impact areas related to food production are: genomic information is required for novel and exotic species before their role in production, conservation or ecosystem sustainability can be understood. The link between genotype and phenotype is not well understood.

39 Development of Breeding Programs for Aquatic Species Should Be Given High Priority, Trygve Gjedrem and Karl Kolstad, September 2012 40 http://cookeaqua.com/ 41 http://www.marineharvestcanada.com/ 42 http://www.icywaters.com/ 43 http://www.mainstreamcanada.com/

Canadian Fisheries & Aquaculture How genomics can address sector challenges 11 • Human health: supporting the establishment of research, which will enable all stakeholders to industry standards, monitoring and product traceabil- understand and base their positions on current ity to ensure biosecurity, and the health impacts scientific knowledge. arising from consuming contaminated products; One argument in favour of selective breeding programs • Resource efficiency and benefit: fish feed is the is that high genetic gain is achievable for disease largest single input in terms of cost. Genomics, and resistance. Examples of this are seen in the Infectious the emerging field of nutrigenomics, are integral Pancreatic Necrosis (IPN) virus in Atlantic salmon, and to the development of new aquatic (seaweed) and bacterial cold water disease in rainbow trout. Application crop-based feeds that move away from the unsus- of genomics and genomics tools to better understand 44 tainable use of fishmeal; and and identify secondary hosts of the MSX (Multinucle- • Biophysical capacity: investigating the efficiencies ated Sphere Unknown) parasite in shellfish would of land, marine and freshwater based systems in have a direct economic impact on the farmed conjunction with targeted species/strains, and industry in Aboriginal and rural communities such as assessing opportunities for both land and off- those in the Bras d’Or Lakes region of Cape Breton. shore-based production. 4.4 Conservation and Population Genomics 4.3 Fish Health The coupling of genomics/functional genomics with Fish resistance or tolerance to disease, pathogens and telemetry has already made a significant impact on our stress is not fully understood. Thus, research is urgently understanding of wild fish migration and established needed on infectious diseases and parasites, thera- real-time genotyping for fish migration. The combina- peutics and vaccine development, interactions tion of watershed-scale biotelemetry and functional between farmed and wild fish, and fin and shellfish genomics has yielded key information of survivorship host/pathogen relationships. of wild salmon. An example is the use of the salmonid microarray developed by the GRASP project to look at Fish in the wild generally have the ability to select factors that may influence migration success in Fraser favourable environments, whereas farmed fish do not River sockeye. This microarray has also been used to and tend to be more vulnerable to disease and stress look at impacts of pathogen carrier status (sea lice situations. The transmission of disease or infection from and IHNv) on wild salmon.45, 46 wild fish to farmed, and vice versa, tends to be a very ‘charged’ subject area and is in need of objective

44 Based strictly on the improvement of feed utilization, it has been estimated that gains made through the national SBP for Atlantic salmon in Norway has saved the Norwegian salmon aquaculture industry $230M p.a. Clearly, the economic gain to the aquaculture sector in Norway is many times this figure when taking into consideration the gains made in growth rate, the reductions in mortality and the other performance and quality improvements that can be attributed to the Norwegian selective breeding programs 45 Developing a Mechanistic Understanding of Fish Migrations by Linking Telemetry with Physiology, Behavior, Genomics and Experimental Biology: An Interdisciplinary Case Study on Adult Fraser River Sockeye Salmon, S.J. Cooke et al., Fisheries, Vol. 33, No. 7, July 2008 46 Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon, Kristina M. Miller et al., Science 333, 214 (2011)

12 Genome Atlantic and Genome British Columbia In order to better understand, predict and manage 4.5 Ecosystem Integrity impacts and benefits in recreational fishing, it is “The idea that a single event or stressor essential that more is learned about the differences is responsible for the 1992-2009 decline at the genome level between domestic/stocked fish in Fraser River sockeye is appealing, but vs. wild populations. improbable. DFO should develop and The lack of genome information in wild fisheries limits carry out a research strategy to assess the the application of genome technologies in the assess- cumulative effects of stressors on Fraser ment of the status and conservation of FiGR. For some River sockeye. DFO science managers species, the limited genetic base from which to draw should encourage innovation and new on for breeding programs and importation or collection research into novel diseases and other 47 of new genetics from the wild is impeded by lack of conditions affecting wild fish.” regulatory clarity on these issues. Other opportunities Species survival and ensuring genetic variation, as for genomics interventions in the area of conservation well as the sustainability of coastal and inland water and population genomics include: ecosystems, is a topic well-suited to a genomics • Wild stock management: monitoring population approach. The aquatic ecosystem is subject to a wide health, species abundance and local population groups range of impacts such as pollution, water salinity, is essential in wild fisheries to avoid overfishing, yet oxygen and acidity levels that in turn place stress on allow a sustainable harvest, and to conserve the fish. For example, salmon reproduction is strongly integrity of the ecosystem; and affected by riverine and estuarine habitat degradation decoupling resource requirements and resource availabil- • Impacts of aquaculture on wild stocks and ity through anthropogenic impacts of agriculture, logging, vice versa: genomics can play a major role in urban expansion, mining, and energy development. determining impacts and finding solutions for factors such as disease and parasites, escapement, Genomics can support the achievement of Canada’s the introduction of novel species, impact of therapeu- sustainability and aquatic biodiversity goals.48 An tics, competition for resources and genetic interactions. example is using a metagenomics approach to under- standing biodiversity in coastal areas and the effect of different environmental stressors, such as finfish and shellfish aquaculture, integrated multitrophic aquacul- ture (IMTA), agricultural run-off, and coastal urban

47 Cohen Commission of Inquiry into the Decline of Sockeye Salmon in the Fraser River, October 2012 48 Sustaining Canadian Marine Biodiversity, an Expert Panel Report on Sustaining Canada's Marine Biodiversity: Responding to the Challenges Posed by Climate Change, Fisheries, and Aquaculture, Prepared by the Royal Society of Canada: The Academies of Arts, Humanities and Sciences of Canada, February 2012

Canadian Fisheries & Aquaculture How genomics can address sector challenges 13 development. Furthermore, the role that fish, shellfish Hence, genomics and its related ethical, environmental, and other organisms play as sentinel species brings economic, legal and social aspects (GE3LS) are integral together for investigation areas such as environmental to the successful application of genomics in the fisheries health, industry impact and ecosystem integrity. and aquaculture sector. A GE3LS approach can address issues such as awareness, engagement, education and 4.6 Social Licence communications and how genomics information can Topics such as the economics of sustainability, societal contribute to informing policy. It can inform and pre- risks, perceived risks and benefits of aspects of the pare the dissemination of evidence-based information, fisheries sector, cultural ties and traditions and/or the prompt outreach to address public perceptions bridg- role of First Nations, West versus East coast cultural, ing the gap between perception and reality, and economic and social priorities, social justice, human provide a channel for public feedback on key issues adaptation to the changing environment, the integration related to the application of genomics. It can also of local and traditional ecological knowledge, raising support the achievement of common understanding stakeholder awareness and information dissemination between diverse communities and cultures. Finally, 3 all come under the banner of ‘social licence’. a GE LS approach can address the economics of genomics tools and their application through cost- benefit study and analysis.

14 Genome Atlantic and Genome British Columbia 5. CANADA’S LEADERSHIP AND STRENGTHS

Canada’s industry and government continues to show “A successful, innovative, dynamic biotech- a commitment to large and small-scale genomics research nology and genomics program to enhance in the fisheries and aquaculture sector. Industry continues the sustainability of our aquatic resources to show its support and confidence in the sector through and the ecological health of our aquatic investments by many companies. Investment by federal ecosystems, that is characterized by strong and provincial government has been substantial, with partnerships and stakeholder involvement; public programming contributing over $130 million to innovative research programs; the applica- date, largely to aquaculture- and capture-based projects. tion of effective biotechnology and genomics Despite the important economic value of recreational tools and products; and funding to maintain fisheries, relatively little has been invested with respect required expertise.” to supporting genomics research. To support this vision, the DFO has invested millions of 5.1 Canada’s Investment dollars in federal genomics R&D since the late 1990s. Furthermore, the DFO’s Aquaculture Collaborative Genome Canada has invested $21.3 million in four Research and Development Program (ACRDP)50 from internationally acclaimed projects. This investment has 2010 to 2011 contributed $32.5 million towards leveraged private sector, and other federal and provincial 326 projects with a total value of $70.0 million—many government program and international funding to achieve of which had a major genomics component. a project total of $43.6 million. In addition, with the support of industry and economic development part- Other programs have supported fisheries and aquaculture ners, Genome Atlantic, Genome BC and Genome projects with genomics content. For example, the Natural Quebec have raised an additional $23M for projects Sciences and Engineering Research Council contributed of importance to both capture and farmed fisheries. $24 million, and the National Research Council’s IRAP program has contributed $3.2 million in support of Biotechnology and genomic tools and products contribute aquaculture SMEs. to the achievement of DFO's priority outcomes and the Department has strategically developed expertise and capabilities in biotechnology and genomics. The vision for DFO’s Aquatic Biotechnology and Genomics Research and Development Strategy 49 is:

49 Aquatic Biotechnology and Genomics Research and Development Strategy, DFO 50 http://www.dfo-mpo.gc.ca/science/enviro/aquaculture/acrdp-pcrda/index-eng.htm

Canadian Fisheries & Aquaculture How genomics can address sector challenges 15 5.2 Canada’s Leadership Brook charr and sablefish. It also continues to be applied to cross-cutting projects that impact both wild Canada’s investments in large-scale genomics projects and farmed stocks such as the DFO’s SLICE® project have resulted in Canada being recognized as a global and Genome BC’s GiLS project. Advances and appli- leader in the genomics of fish and shellfish, and has cation developments in biotechnology and genomics contributed significantly to the ranking of the quality of present the potential of low-cost biotechnology appli- Agriculture, Fisheries and Forestry research as second in cations with greater sensitivity, accuracy, faster results the world—behind the U.S.51 This research excellence and and increased efficiency. capacity is supported by a first rate research infrastruc- ture that encompasses universities, research institutes, Canada’s research capacity, by supporting high-growth federal research labs, companies and technologies. strategies through the application of next generation genomics technologies; improving product quality, Cutting-edge research continues to be conducted on production efficiency, and environmental sustainability the application of genomics to traditional species such of farmed species; and ensuring wild species conser- as cod, halibut, salmonids such as Pacific and Atlantic vation and protecting ecosystem biodiversity, works to salmon, trout and whitefish, eels, and emerging spe- give Canadian fisheries and aquaculture a competitive cies of economic importance such as Arctic charr, advantage in the global market.

51 The State of Science and Technology in Canada, 2012, Council of Canadian Academies

16 Genome Atlantic and Genome British Columbia 6. SUCCESS OF PAST CANADIAN INVESTMENTS IN FISHERIES & AQUACULTURE GENOMICS The genomic sciences continue to form a significant • The Genomics Research on Atlantic Salmon component of Canada’s research program and Cana- Project (GRASP) and Consortium for Genomic dian genomics research can point to important Research on all Salmonids Project (cGRASP) successes in: projects, which have produced many genomics tools and resources for salmonids, including gene lists, • Disease Resistance: the development, through genetic markers and microarrays. The Atlantic marker-assisted selection, of IPN resistant strains salmon genome sequence will also act as a refer- of Atlantic salmon was achieved through the ence genome for other salmonids;53, 54 and genomic identification of quantitative trait loci (QTL) that confer resistance; • Pleurogene—Flatfish genomics: enhancing commercial culture of Atlantic halibut and • Population Health: the identification of a genomic Senegal sole was a partnership between Genome signature associated with increased mortality in Canada and Genoma España and produced the migrating Fraser River Sockeye salmon; world’s first genetic linkage map of Atlantic halibut. • Stock Management: the microarray chip developed This gave Canadian producers a key tool for improv- by the GRASP and cGRASP projects is used in over ing productivity and competitiveness by increasing 70 labs worldwide and by the DFO to monitor wild broodstock development capabilities.55 salmon stocks; and Smaller-scale research projects continue to be • Production Efficiency: a 20% reduction in grow undertaken and demonstrate a mix of innovation, out time to market for halibut came as a direct leading-edge expertise, industry partnering, the use impact from the Pleurogene project. of advanced genomics technologies, and diversifica- Genome Canada, in partnership with Genome tion of the range of species. Examples include: Atlantic, Genome BC and Genome Quebec, as • Genomics in Lice and Salmon (GiLS): Sea lice well as regional economic development agencies infections of salmon populations threaten an import- and industry, has supported: ant economic and environmental resource in BC. • The Atlantic Cod Genomics and Broodstock GiLS made use of genomics to understand the host- Project (CGP) has contributed to cod aquaculture pathogen interaction between different salmon 56 through the identification of genetic markers, and populations and lice; the construction and development of genetic maps and tools for marker-assisted selection (MAS);52

52 http://www.genomeatlantic.ca/projects/view/8-The_Atlantic_Cod_Genomics_and_Broodstock_Development_Project_CGP 53 http://www.genomebc.ca/portfolio/projects/fisheries-projects/completed/genomics-research-on-atlantic-salmon-project-grasp/ 54 http://www.genomebc.ca/portfolio/projects/fisheries-projects/completed/consortium-for-genomic-research-on-all-salmonids- project-cgrasp/ 55 http://www.genomeatlantic.ca/projects/view/6-Pleurogene_Flatfish_genomics_enhancing_commercial_culture_of_Atlantic_ halibut_and_Senegal_sole 56 http://www.genomebc.ca/portfolio/projects/fisheries-projects/genomics-in-lice-and-salmon-gils/

Canadian Fisheries & Aquaculture How genomics can address sector challenges 17 • TREAT2—the development of sustainable • Sablefish Genomics:sablefish is an economically treatments targeted at sea lice infestations in important species in commercial fisheries of the cultured salmon: supported with funding by the North Pacific and an emerging species in aquacul- Atlantic Canada Opportunities Agency’s Atlantic ture. The industry is valued at over $300 million Innovation Fund and led by Novartis Animal Health in North America, yet, to date, little was known Canada with partners Atlantic Veterinary College - about its genetics. This project undertook a preliminary University of Prince Edward Island, University of characterization of genetic markers. The resultant Guelph and the University of Victoria; genetic map is thought to represent the first linkage • Atlantic salmon: Mainstream Canada, Simon map for a member of the Scorpaeniformes and will Fraser University (SFU)57 and CIGENE, Norway58 allow for the successful development of future brood- 62, 63, 64 are working on MAS to identify quantitative trait stock and mapping of phenotypes of interest; loci (QTL)59 associated with body-weight traits;60 • Genomic Tools for Fisheries Management • Arctic charr: Icy Waters Ltd. has developed a strong (FishMan Omics): this project will identify bio- broodstock program in collaboration with SFU. The markers and use them to assess the overall health 65 company’s current focus is the discovery of genetic and condition of migrating wild salmon fish stocks; markers associated with disease and stress; the • Development of a health assessment tool for Institut de recherché sur les zone côtières, Université marine mussels (Myt_OME): the project developed de Moncton61 was awarded funding under the 2011 genomic resources and tools for two commercially Round of the Atlantic Innovation Fund to create a important species of marine mussels, thus enabling national Arctic charr genetic improvement program; more accurate health assessments of coastal zones

57 http://www.sfu.ca/ 58 http://www.cigene.no/ 59 Quantitative trait loci (QTLs) are stretches of DNA containing or linked to the genes that underlie a quantitative trait. 60 Genetic Mapping of Quantitative Trait Loci (QTL) for Body-Weight in Atlantic Salmon (Salmo Salar) Using a 6.5K SNP Array, Aquaculture 358-359 (2012) 61-70 61 http://www.umoncton.ca/ 62 Application of Genome Science to Sustainable Aquaculture, Proceedings of a special session held at Aquaculture Canada, 2009 63 http://www.genomebc.ca/portfolio/projects/fisheries-projects/completed/sablefish-genomics/ 64 Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene, Rondeau et al. BMC Genomics 2013, 14:452 65 http://www.genomebc.ca/portfolio/projects/fisheries-projects/genomic-tools-for-fisheries-management-fishman-omics/

18 Genome Atlantic and Genome British Columbia and facilitating the ability to monitor the effects of including MSX, listed as reportable or immediately the changing environment;66 and notifiable in the Health of Animals Act68; the Aquatic • GreenSNPs: an enabling technology for Wildlife Division (AWD, Quebec) has started to include environmental genomics in aquatic or land genomic tools in its current practices and has put in animals and plants: one of the activities of this place the mapping and monitoring of Quebec’s salmon project is centered on the American eel with impacts and trout populations using population genetics; on the management of exploited stocks, aquaculture Genome BC has partnered with Chile and Norway in development, and environmental health related to an International Cooperation to Sequence the Atlantic effects of pollutants.67 Salmon Genome; and Genome Atlantic has supported the Camelina: Developing Canada’s Next Oilseed In other innovative developments, DFO’s National Project, which aims to develop a crop-based, low-cost Aquatic Animal Health Program (with laboratories in alternate to . Moncton, Winnipeg and Nanaimo) uses molecular techniques to develop validated tests for diseases,

66 http://www.genomebc.ca/portfolio/projects/fisheries-projects/genomic-tools-for-fisheries-management-fishman-omics/ 67 http://www.genomequebec.com/en/your-environment.html 68 http://laws-lois.justice.gc.ca/eng/acts/H-3.3/

Canadian Fisheries & Aquaculture How genomics can address sector challenges 19 7. the SOCIO-ECONOMIC IMPACT OF SUCCESSFUL GENOMICS ENABLED SOLUTIONS The fisheries and aquaculture sector is vulnerable to 7.1 Commercial Fisheries often competing natural, socio-economic, political, 7.1.1 Capture Fisheries environmental and technological forces. The success- ful application of genomics, whether in breeding Capture fisheries provides employment for over programs, stocking management, population genetics, 50,000 people, largely in rural, coastal and Aboriginal reduced inputs, disease management and prevention, communities. Key to a stable capture fishery is the conserving biodiversity or ecosystem management, management and conservation of a diverse range will have a direct impact on provincial and national of capture FiGR while simultaneously exploiting, in economies, and the Canadian aquatic ecosystem. a sustainable manner, the potential of indigenous crustacean, shellfish and finfish populations such Genomics research, and the application of genome- as Arctic charr, trout, whitefish, walleye and sablefish. based tools, can provide insights to complex aquatic This is a key socio-economic impact and a driver of challenges and support the sustainable development genomics research. and management of this important resource. In doing so, it will contribute to: rural, coastal and Aboriginal To accomplish this, good information on areas such as community economic development; industry growth species origin, population genetic diversity, and popula- and international competitiveness; an understanding tion migration is vital. Research is needed to provide of the interactions and impacts between recreational, reliable information that will help address serious capture and farmed fisheries; an informed policy and issues such as escapement and disease transfer, and regulatory environment resulting in effective fisheries can support the promotion of evidence-based dialogue management planning; and a thriving and sustainable between capture and farmed fisheries. national aquatic resource. 7.1.2 Aquaculture Furthermore, in the specific area of social licence, the GE3LS component is a critical mechanism for The genome sciences can directly impact the ensuring that all stakeholders fully understand their socio-economic well-being of Canadians by roles and responsibilities and the social, ethical, regula- supporting the efficient and profitable production tory and environmental impacts of genomics-based of high-quality protein in a safe, secure and sustain- approaches; that the data is seen as transparent and able manner. In 1986, Canadian aquaculture objective; and that the evidence of these impacts are production amounted to only 10,488 tonnes, valued widely available. at $35 million; by 2006, production had grown to 171,829 tonnes with a value of over $912 million. Aquaculture now accounts for 14% of total Canadian fisheries production and 33% of its value. Farmed

20 Genome Atlantic and Genome British Columbia salmon is British Columbia’s largest agricultural export and Aboriginal communities such as Charlotte County, product, and the largest crop in the New Brunswick NB, and Ahousaht (Ahousaht First Nation), Tsaxana agri-food sector. Over 8,000 Canadians are directly (Mowachaht Muchalaht First Nations), and Klemtu employed in aquaculture—most of them full time. The (Kitasoo First Nation) in BC, among many others.72 aquaculture supply and services sector creates an Much of the employment growth in communities such additional 8,000 jobs. Two-thirds of all workers are as these can be attributed to the expansion of the under the age of 35.69 aquaculture industry as other sectors have stabilized or declined. A successful aquaculture industry attracts In a highly competitive market, finding the most efficient investment, increases social well-being within rural manner to operate profitably while being environmen- and coastal communities, and helps retain and attract tally and socially responsible will ensure the long-term young people to the community by offering a wide viability of the Canadian farmed fish and shellfish range of skilled employment opportunities. industry.70 Successful genomics-based applications, such as SBPs and MAS, will provide industry with the 7.2 Recreational Fisheries tools needed to support production growth and enable it to compete with greater success for global market Recreational fisheries is a highly dispersed, community- share. The application of the genome sciences to based activity with international appeal and a clear the complexities of the aquatic ecosystem will also source of wealth, jobs and investment for rural com- provide hard data for the management and regulation munities as well as tax revenues for provincial and of the industry. federal governments. To ensure continued socio-economic benefits from this sector, our lack of understanding of Aquaculture has proven economic benefits within each anthropogenic, climate change, stocking, ‘catch and province and nationally. An increased economic benefit release’, and biodiversity (local population groups) in one province will therefore have substantial eco- impacts on the aquatic ecosystem, will need to nomic impacts nationally.71 The industry has positive be addressed. socio-economic impacts, particularly in rural, coastal

69 Canadian Aquaculture: An Important Economic Contributor , http://www.aquaculture.ca/files/economic-benefits.php 70 Report to Launch the Aquaculture Sustainability Reporting Initiative, DFO, 2010 71 Socio-Economic Impact of Aquaculture in Canada; prepared for Fisheries and Oceans Canada by Gardner Pinfold Consulting Economists Ltd., 2010 72 http://www.dfo-mpo.gc.ca/aquaculture/ref/aqua-es2009-eng.htm#ch22

Canadian Fisheries & Aquaculture How genomics can address sector challenges 21 8. NEXT STEPS TOWARD SUCCESS

“Genomics—a vital link in the future success growth. This growth should balance the needs of of Canadian fisheries and aquaculture” industry for efficient and profitable protein production, with the management and conservation of wild stocks— From the fisheries and aquaculture workshop, there commercial and non-commercial, and associated was a consensus among industry and academia that marine ecosystems. Canada needs a national strategy for the fisheries and aquaculture sector. Such a strategy would address Discussions at the national fisheries and aquaculture challenges such as sector fragmentation and coordina- workshop generated a fertile base of research ideas, tion, sustainability for each stakeholder unit, an economic as well as identifying, confirming and augmenting model for fisheries, the need for a long-term funding the sectoral challenges and opportunities previously model, and realistic expectations and timelines for the identified in the consultation process and strategy impact of key drivers, such as genomics. While recog- development. The content of these dialogues provide nizing that this may be a longer-term aspiration, what a solid platform that the fisheries and aquaculture sector can be achieved in the short-term is an agreed Genomics can build on and identify as its “next steps towards Strategy for Canadian Fisheries and Aquaculture. success”. While the diversity and range of research proposed was considerable, five key themes where an This national genomics strategy should focus on giving investment in genomics would ensure sustainable industry, academia and government the tools to propel sector growth and national leadership were apparent: Canada to sustainable international leadership in the essential, but highly competitive, global fisheries and 1. Translational or outcomes-based research: aquaculture sector. Building on the capacity and industry and academia agree that there is a require- infrastructure generated through previous investments, ment for understanding the genomes of traditional, the genome sciences can help support and maintain novel and invasive species. This ranges from Canada’s competitiveness against jurisdictions such as determining reference genomes that provide the Europe and Chile, who continue to invest heavily in the foundation for future work, to the identification of use of genomics in national aquaculture breeding biomarkers for desirable traits such as disease programs, and in capture fisheries through projects susceptibility, species origin, and carcass quality such as AquaTrace73, FishTrace74, and SALSEA75. in commercial and non-commercial fisheries. Basic research also extends to understanding To be effective in defending and exploiting Canada’s organisms in the associated ecosystems and their aquatic ecosystem, there will need to be productive ecosystem interactions. collaborations between a diverse range of stakehold- ers and interest groups including industry, academia, There is a lack of understanding of the genomics government, First Nations, consumers and the general of shellfish (including lobster). Given the rapid rise public, underpinned by compelling communications in shellfish production and its increasing importance and education. as an industry sector, there is a priority need to address this knowledge gap, especially with respect Nationally, genomics can make a beneficial social and to broodstock development, early maturation and economic impact by supporting sustainable sector disease resistance;

73 https://aquatrace.eu/ 74 https://fishtrace.jrc.ec.europa.eu/fishtrace/composite.action 75 http://www.nasco.int/sas/salsea.htm

22 Genome Atlantic and Genome British Columbia 2. Genomics tools: practical, affordable, and trusted of phenotype-genotype linkages. Understanding “in-field” genomic diagnostics are needed at all and alleviating the stress of fish populations was levels of the sector. Such tools would have wide identified of particular importance for aquaculture. application not only in wild, capture, recreational and farmed stock monitoring, tracking and manage- To underpin and increase the effectiveness of the ment, but also in the regulatory field, e.g., by DFO; application of genomics to fisheries and aquaculture, there are a select number of areas that need to 3. Health and nutrition: health and nutrition is a be considered: cross-cutting research theme that can ensure the conservation of wild stocks and satisfy the needs • Communications and education: at all levels of of consumers for quality protein. Investment is the sector value chain, and within many stakeholder needed to understand and determine the genomics or interest groups, there is a low level of understanding of disease and parasite infestation and the produc- of the utility or value of genomics. A comprehensive, tion of targeted, environmentally friendly treatments, ongoing public communications, dissemination and e.g., vaccines; to optimize sustainable diet and education strategy is required to support social nutrition characteristics; and to understand the licence, highlight benefits and dispel inadequate causes and socio-economic impacts of environ- and/or misinformation. Such a strategy will require mental and production stress on species. Health a commitment to identifying and responding to and nutrition is a needed focus with practical the priorities and needs of the public, and other application in the short- and longer-terms; user groups. • Building trust: to be effective, genomics research, 4. Species sustainability: ensuring the survival and its application, has to be seen as objective by and conservation of aquatic species—both fin and industry, academia, the public and government. shellfish—is vital to the growth of the Canadian Achieving this will entail creating a platform to encour- fisheries and aquaculture sector and a thriving age transparency in the generation, publication and aquatic ecosystem. Key focus areas for research use of data, and for data sharing. It will also require highlighted by the workshop include: understanding the development of models for structured collabora- population management units and stock structure; tion, particularly between industry and academia, and the interaction between wild and farmed species; the recruitment of committed, sector champions. disease, parasite and pathogen transportation; tracking species mortality; and the impact of climate In conclusion, the consultation process that has change and anthropogenic stressors on the aquatic accompanied and provided a mine of goodwill, environment—oceans, rivers and inland waters; and information, and comment for the Fisheries and Aquaculture Genomics Sector Strategy Paper 5. Breeding programs: breeding programs are has been a positive, constructive step in the evolution essential for effective management, species planning of an impactful national strategy that makes the best and control of the outputs from farms. This applies use of Canadian genomics expertise and industry to the production of high-quality seedstock for leadership, while building social licence through hatcheries, to elite broodstock for the aquaculture effective communications and education. industry and to restocking programs in recreational fisheries. Selective breeding programs allow the validation of biomarkers for key production, stress and disease susceptibility traits, and the elucidation

Canadian Fisheries & Aquaculture How genomics can address sector challenges 23 ACKNOWLEDGEMENTS

Thanks are due to the members of the national steering We deeply appreciate the support and input from committee of government, academic and industry industry, academia and government who attended representatives, which was assembled to support the the national workshop and to those who provided development of the Fisheries and Aquaculture Genomics feedback during the workshop pre-consultation. Sector Strategy Paper. The committee members were: The Genome Centre contributors to the management • Louis Bernatchez, Chaire de recherche du Canada of the strategy development process and the organiza- en Génomique et Conservation des Ressources tion and delivery of the national workshop were key to Aquatiques, Université Laval, QC, the success of this initiative. They include:

• Brian Blanchard, VP and General Manager, • Steven Armstrong, President and CEO, Scotian Halibut Ltd., NS, Genome Atlantic, • Jason Cleaversmith, Head of Aqua Health PEI, • Shelley King, VP Research and Development, Novartis Animal Health, Genome Atlantic, • William S. Davidson, Professor, Department of • Sue Coueslan, Director of External Relations, Molecular Biology and Biochemistry, Simon Fraser Genome Atlantic, University, BC, • Gabe Kalmar, Vice President, Sector Development, • Jessy Dynes, Chef de Service, Service de la faune Genome British Columbia, aquatique, Ministère des Ressources naturelles et de la Faune du Quebec, QC, • Tony Brooks, Chief Financial Officer, Genome British Columbia, • Ben Koop, Professor, Faculty in Biology, University of Victoria, BC, • Rachael Ritchie, Director, Business Development, Genome British Columbia, and • Jay Parsons, Director, Department of Fisheries and Oceans—Aquaculture and Science Branch, ON, • Catalina Lopez-Correa, VP Scientific Affairs, Genome Quebec. • Debbie Plouffe, Vice President Research, Center for Aquaculture Technologies Canada, PEI, Finally, our thanks to David Millar, Executive Chairman, • Brian Riddell, Chief Executive Officer, Haisley Millar Consulting Group, TX who provided Pacific Salmon Foundation, BC, support in the researching and drafting of the paper and delivery of the pre-consultation process; and to • Ed Safarik, Former President and CEO, Ocean the staff from Genome Atlantic (David Spurrell and Fisheries Ltd., and Board Member of Genome BC, Kim Johnstone) who assisted in providing reference • Brian Skinner, ingénieur forestier, Ministère des sources and publications. Ressources naturelles et de la Faune du Quebec, QC, and • Mary Ellen Walling, Executive Director, BC Salmon Farmers Association, BC.

24 Genome Atlantic and Genome British Columbia For more information contact:

Genome Canada Ontario Genomics Institute Cindy Bell Alison Symington Executive Vice-President, Corporate Development Vice President, Corporate Development Tel.: 613-751-4460, ext. 218 416-673-6594 [email protected] [email protected] www.genomecanada.ca www.ontariogenomics.ca

Genome British Columbia Genome Quebec Gabe Kalmar Catalina López-Correa Vice President, Sector Development Vice President, Scientific Affairs Tel.: 604-637-4374 Tel.: 514-398-0668 [email protected] [email protected] www.genomebc.ca www.genomequebec.com

Genome Alberta Genome Atlantic Gijs van Rooijen Shelley King Chief Scientific Officer Vice President, Research and Business Development Tel.: 403-210-5253 Tel.: 902-421-5646 [email protected] [email protected] www.genomealberta.ca www.genomeatlantic.ca

Genome Prairie Chris Barker Chief Scientific Officer Tel.: 306-668-3587 [email protected] www.genomeprairie.ca